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Book ; Online: Comparative Study of Pre-Trained BERT Models for Code-Mixed Hindi-English Data

Patil, Aryan / Patwardhan, Varad / Phaltankar, Abhishek / Takawane, Gauri / Joshi, Raviraj

2023

Abstract: The term "Code Mixed" refers to the use of more than one language in the same text. This phenomenon is predominantly observed on social media platforms, with an increasing amount of adaptation as time goes on. It is critical to detect foreign elements in ...

Abstract	The term "Code Mixed" refers to the use of more than one language in the same text. This phenomenon is predominantly observed on social media platforms, with an increasing amount of adaptation as time goes on. It is critical to detect foreign elements in a language and process them correctly, as a considerable number of individuals are using code-mixed languages that could not be comprehended by understanding one of those languages. In this work, we focus on low-resource Hindi-English code-mixed language and enhancing the performance of different code-mixed natural language processing tasks such as sentiment analysis, emotion recognition, and hate speech identification. We perform a comparative analysis of different Transformer-based language Models pre-trained using unsupervised approaches. We have included the code-mixed models like HingBERT, HingRoBERTa, HingRoBERTa-Mixed, mBERT, and non-code-mixed models like AlBERT, BERT, and RoBERTa for comparative analysis of code-mixed Hindi-English downstream tasks. We report state-of-the-art results on respective datasets using HingBERT-based models which are specifically pre-trained on real code-mixed text. Our HingBERT-based models provide significant improvements thus highlighting the poor performance of vanilla BERT models on code-mixed text. Comment: Accepted at IEEE 8th International Conference for Convergence in Technology
Keywords	Computer Science - Computation and Language ; Computer Science - Machine Learning
Publishing date	2023-05-25
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Unzipping hBN with ultrashort mid-infrared pulses.

Chen, Cecilia Y / Moore, Samuel L / Maiti, Rishi / Ginsberg, Jared S / Jadidi, M Mehdi / Li, Baichang / Chae, Sang Hoon / Rajendran, Anjaly / Patwardhan, Gauri N / Watanabe, Kenji / Taniguchi, Takashi / Hone, James / Basov, D N / Gaeta, Alexander L

Science advances

2024 Volume 10, Issue 18, Page(s) eadi3653

Abstract: Manipulating the nanostructure of materials is critical for numerous applications in electronics, magnetics, and photonics. However, conventional methods such as lithography and laser writing require cleanroom facilities or leave residue. We describe an ... ...

Abstract	Manipulating the nanostructure of materials is critical for numerous applications in electronics, magnetics, and photonics. However, conventional methods such as lithography and laser writing require cleanroom facilities or leave residue. We describe an approach to creating atomically sharp line defects in hexagonal boron nitride (hBN) at room temperature by direct optical phonon excitation with a mid-infrared pulsed laser from free space. We term this phenomenon "unzipping" to describe the rapid formation and growth of a crack tens of nanometers wide from a point within the laser-driven region. Formation of these features is attributed to the large atomic displacement and high local bond strain produced by strongly driving the crystal at a natural resonance. This process occurs only via coherent phonon excitation and is highly sensitive to the relative orientation of the crystal axes and the laser polarization. Its cleanliness, directionality, and sharpness enable applications such as polariton cavities, phonon-wave coupling, and in situ flake cleaving.
Language	English
Publishing date	2024-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adi3653
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Leveraging Language Identification to Enhance Code-Mixed Text Classification

Takawane, Gauri / Phaltankar, Abhishek / Patwardhan, Varad / Patil, Aryan / Joshi, Raviraj / Takalikar, Mukta S.

2023

Abstract: The usage of more than one language in the same text is referred to as Code Mixed. It is evident that there is a growing degree of adaption of the use of code-mixed data, especially English with a regional language, on social media platforms. Existing ... ...

Abstract	The usage of more than one language in the same text is referred to as Code Mixed. It is evident that there is a growing degree of adaption of the use of code-mixed data, especially English with a regional language, on social media platforms. Existing deep-learning models do not take advantage of the implicit language information in the code-mixed text. Our study aims to improve BERT-based models performance on low-resource Code-Mixed Hindi-English Datasets by experimenting with language augmentation approaches. We propose a pipeline to improve code-mixed systems that comprise data preprocessing, word-level language identification, language augmentation, and model training on downstream tasks like sentiment analysis. For language augmentation in BERT models, we explore word-level interleaving and post-sentence placement of language information. We have examined the performance of vanilla BERT-based models and their code-mixed HingBERT counterparts on respective benchmark datasets, comparing their results with and without using word-level language information. The models were evaluated using metrics such as accuracy, precision, recall, and F1 score. Our findings show that the proposed language augmentation approaches work well across different BERT models. We demonstrate the importance of augmenting code-mixed text with language information on five different code-mixed Hindi-English downstream datasets based on sentiment analysis, hate speech detection, and emotion detection.
Keywords	Computer Science - Computation and Language ; Computer Science - Machine Learning
Subject code	420
Publishing date	2023-06-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations.

Patwardhan, Gauri A / Marczyk, Michal / Wali, Vikram B / Stern, David F / Pusztai, Lajos / Hatzis, Christos

NPJ breast cancer

2021 Volume 7, Issue 1, Page(s) 60

Abstract: The effect of scheduling of targeted therapy combinations on drug resistance is underexplored in triple-negative breast cancer (TNBC). TNBC constitutes heterogeneous cancer cell populations the composition of which can change dynamically during treatment ...

Abstract	The effect of scheduling of targeted therapy combinations on drug resistance is underexplored in triple-negative breast cancer (TNBC). TNBC constitutes heterogeneous cancer cell populations the composition of which can change dynamically during treatment resulting in the selection of resistant clones with a fitness advantage. We evaluated crizotinib (ALK/MET inhibitor) and navitoclax (ABT-263; Bcl-2/Bcl-xL inhibitor) combinations in a large design consisting of 696 two-cycle sequential and concomitant treatment regimens with varying treatment dose, duration, and drug holiday length over a 26-day period in MDA-MB-231 TNBC cells and found that patterns of resistance depend on the schedule and sequence in which the drugs are given. Further, we tracked the clonal dynamics and mechanisms of resistance using DNA-integrated barcodes and single-cell RNA sequencing. Our study suggests that longer formats of treatment schedules in vitro screening assays are required to understand the effects of resistance and guide more realistically in vivo and clinical studies.
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article
ISSN	2374-4677
ISSN	2374-4677
DOI	10.1038/s41523-021-00270-4
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Article ; Online: Phonon-enhanced nonlinearities in hexagonal boron nitride.

Ginsberg, Jared S / Jadidi, M Mehdi / Zhang, Jin / Chen, Cecilia Y / Tancogne-Dejean, Nicolas / Chae, Sang Hoon / Patwardhan, Gauri N / Xian, Lede / Watanabe, Kenji / Taniguchi, Takashi / Hone, James / Rubio, Angel / Gaeta, Alexander L

Nature communications

2023 Volume 14, Issue 1, Page(s) 7685

Abstract: Polar crystals can be driven into collective oscillations by optical fields tuned to precise resonance frequencies. As the amplitude of the excited phonon modes increases, novel processes scaling non-linearly with the applied fields begin to contribute ... ...

Abstract	Polar crystals can be driven into collective oscillations by optical fields tuned to precise resonance frequencies. As the amplitude of the excited phonon modes increases, novel processes scaling non-linearly with the applied fields begin to contribute to the dynamics of the atomic system. Here we show two such optical nonlinearities that are induced and enhanced by the strong phonon resonance in the van der Waals crystal hexagonal boron nitride (hBN). We predict and observe large sub-picosecond duration signals due to four-wave mixing (FWM) during resonant excitation. The resulting FWM signal allows for time-resolved observation of the crystal motion. In addition, we observe enhancements of third-harmonic generation with resonant pumping at the hBN transverse optical phonon. Phonon-induced nonlinear enhancements are also predicted to yield large increases in high-harmonic efficiencies beyond the third.
Language	English
Publishing date	2023-11-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43501-x
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Article ; Online: Sphingolipids and mitochondrial apoptosis.

Patwardhan, Gauri A / Beverly, Levi J / Siskind, Leah J

Journal of bioenergetics and biomembranes

2016 Volume 48, Issue 2, Page(s) 153–168

Abstract: The sphingolipid family of lipids modulate several cellular processes, including proliferation, cell cycle regulation, inflammatory signaling pathways, and cell death. Several members of the sphingolipid pathway have opposing functions and thus ... ...

Abstract	The sphingolipid family of lipids modulate several cellular processes, including proliferation, cell cycle regulation, inflammatory signaling pathways, and cell death. Several members of the sphingolipid pathway have opposing functions and thus imbalances in sphingolipid metabolism result in deregulated cellular processes, which cause or contribute to diseases and disorders in humans. A key cellular process regulated by sphingolipids is apoptosis, or programmed cell death. Sphingolipids play an important role in both extrinsic and intrinsic apoptotic pathways depending on the stimuli, cell type and cellular response to the stress. During mitochondrial-mediated apoptosis, multiple pathways converge on mitochondria and induce mitochondrial outer membrane permeabilization (MOMP). MOMP results in the release of intermembrane space proteins such as cytochrome c and Apaf1 into the cytosol where they activate the caspases and DNases that execute cell death. The precise molecular components of the pore(s) responsible for MOMP are unknown, but sphingolipids are thought to play a role. Here, we review evidence for a role of sphingolipids in the induction of mitochondrial-mediated apoptosis with a focus on potential underlying molecular mechanisms by which altered sphingolipid metabolism indirectly or directly induce MOMP. Data available on these mechanisms is reviewed, and the focus and limitations of previous and current studies are discussed to present important unanswered questions and potential future directions.
MeSH term(s)	Animals ; Apoptosis/physiology ; Apoptotic Protease-Activating Factor 1/genetics ; Apoptotic Protease-Activating Factor 1/metabolism ; Humans ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Permeability ; Sphingolipids/genetics ; Sphingolipids/metabolism
Chemical Substances	APAF1 protein, human ; Apoptotic Protease-Activating Factor 1 ; Sphingolipids
Language	English
Publishing date	2016-04
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	198499-8
ISSN	1573-6881 ; 0145-479X ; 0449-5705
ISSN (online)	1573-6881
ISSN	0145-479X ; 0449-5705
DOI	10.1007/s10863-015-9602-3
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Article ; Online: Sphingolipids and expression regulation of genes in cancer.

Patwardhan, Gauri A / Liu, Yong-Yu

Progress in lipid research

2010 Volume 50, Issue 1, Page(s) 104–114

Abstract: Sphingolipids including glycosphingolipids have myriad effects on cell functions and affect cancer in aspects of tumorigenesis, metastasis and tumor response to treatments. Bioactive ones like ceramide, sphingosine 1-phosphate and globotriaosylceramide ... ...

Abstract	Sphingolipids including glycosphingolipids have myriad effects on cell functions and affect cancer in aspects of tumorigenesis, metastasis and tumor response to treatments. Bioactive ones like ceramide, sphingosine 1-phosphate and globotriaosylceramide initiate and process cellular signaling to alter cell behaviors immediately responding to oncogenic stress or treatment challenges. Recent studies pinpoint that sphingolipid-mediated gene expression has long and profound impacts on cancer cells, and these play crucial roles in tumor progression and in treatment outcome. More than 10 sphingolipids and glycosphingolipids selectively mediate expressions of approximately 50 genes including c-myc, p21, c-fos, telomerase reverse transcriptase, caspase-9, Bcl-x, cyclooxygenase-2, matrix metalloproteinases, integrins, Oct-4, glucosylceramide synthase and multidrug-resistant gene 1. By diverse functions of these genes, sphingolipids enduringly affect cellular processes of mitosis, apoptosis, migration, stemness of cancer stem cells and cellular resistance to therapies. Mechanistic studies indicate that sphingolipids regulate particular gene expression by modulating phosphorylation and acetylation of proteins that serve as transcription factors (β-catenin, Sp1), repressor of transcription (histone H3), and regulators (SRp30a) in RNA splicing. Disclosing molecular mechanisms by which sphingolipids selectively regulate particular gene expression, instead of other relevant ones, requires understanding of the exact roles of individual lipid instead of a group, the signaling pathways that are implicated in and interaction with proteins or other lipids in details. These studies not only expand our knowledge of sphingolipids, but can also suggest novel targets for cancer treatments.
MeSH term(s)	Animals ; Gene Expression Regulation, Neoplastic ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Sphingolipids/metabolism
Chemical Substances	Sphingolipids
Language	English
Publishing date	2010-10-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	282560-0
ISSN	1873-2194 ; 0079-6832 ; 0163-7827
ISSN (online)	1873-2194
ISSN	0079-6832 ; 0163-7827
DOI	10.1016/j.plipres.2010.10.003
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Book ; Online: Unzipping hBN with ultrashort mid-infrared pulses

Chen, Cecilia Y. / Ginsberg, Jared S. / Moore, Samuel L. / Jadidi, M. Mehdi / Maiti, Rishi / Li, Baichang / Chae, Sang Hoon / Rajendran, Anjaly / Patwardhan, Gauri N. / Watanabe, Kenji / Taniguchi, Takashi / Hone, James / Basov, D. N. / Gaeta, Alexander L.

2022

Abstract: Manipulating the nanostructure of materials is critical for numerous applications in electronics, magnetics, and photonics. However, conventional methods such as lithography and laser-writing require cleanroom facilities or leave residue. Here, we ... ...

Abstract	Manipulating the nanostructure of materials is critical for numerous applications in electronics, magnetics, and photonics. However, conventional methods such as lithography and laser-writing require cleanroom facilities or leave residue. Here, we describe a new approach to create atomically sharp line defects in hexagonal boron nitride (hBN) at room temperature by direct optical phonon excitation in the mid-infrared (mid-IR). We term this phenomenon "unzipping" to describe the rapid formation and growth of a <30-nm-wide crack from a point within the laser-driven region. The formation of these features is attributed to large atomic displacements and high local bond strain from driving the crystal at a natural resonance. This process is distinguished by (i) occurring only under resonant phonon excitation, (ii) producing highly sub-wavelength features, and (iii) sensitivity to crystal orientation and pump laser polarization. Its cleanliness, directionality, and sharpness enable applications in in-situ flake cleaving and phonon-wave-coupling via free space optical excitation. Comment: 11 pages, 4 figures
Keywords	Condensed Matter - Materials Science ; Physics - Optics
Subject code	535
Publishing date	2022-05-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells.

Marczyk, Michal / Patwardhan, Gauri A / Zhao, Jun / Qu, Rihao / Li, Xiaotong / Wali, Vikram B / Gupta, Abhishek K / Pillai, Manoj M / Kluger, Yuval / Yan, Qin / Hatzis, Christos / Pusztai, Lajos / Gunasekharan, Vignesh

Cancers

2020 Volume 12, Issue 9

Abstract: Cancer cells employ various defense mechanisms against drug-induced cell death. Investigating multi-omics landscapes of cancer cells before and after treatment can reveal resistance mechanisms and inform new therapeutic strategies. We assessed the ... ...

Abstract	Cancer cells employ various defense mechanisms against drug-induced cell death. Investigating multi-omics landscapes of cancer cells before and after treatment can reveal resistance mechanisms and inform new therapeutic strategies. We assessed the effects of navitoclax, a BCL2 family inhibitor, on the transcriptome, methylome, chromatin structure, and copy number variations of MDA-MB-231 triple-negative breast cancer (TNBC) cells. Cells were sampled before treatment, at 72 h of exposure, and after 10-day drug-free recovery from treatment. We observed transient alterations in the expression of stress response genes that were accompanied by corresponding changes in chromatin accessibility. Most of these changes returned to baseline after the recovery period. We also detected lasting alterations in methylation states and genome structure that suggest permanent changes in cell population composition. Using single-cell analyses, we identified 2350 genes significantly upregulated in navitoclax-resistant cells and derived an 18-gene navitoclax resistance signature. We assessed the navitoclax-response-predictive function of this signature in four additional TNBC cell lines in vitro and in silico in 619 cell lines treated with 251 different drugs. We observed a drug-specific predictive value in both experiments, suggesting that this signature could help guiding clinical biomarker studies involving navitoclax.
Language	English
Publishing date	2020-09-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers12092551
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Article: Sphingolipids and expression regulation of genes in cancer

Patwardhan, Gauri A / Liu, Yong-Yu

Progress in Lipid Research. 2011 Jan., v. 50, no. 1

2011

Abstract	Sphingolipids including glycosphingolipids have myriad effects on cell functions and affect cancer in aspects of tumorigenesis, metastasis and tumor response to treatments. Bioactive ones like ceramide, sphingosine 1-phosphate and globotriaosylceramide initiate and process cellular signaling to alter cell behaviors immediately responding to oncogenic stress or treatment challenges. Recent studies pinpoint that sphingolipid-mediated gene expression has long and profound impacts on cancer cells, and these play crucial roles in tumor progression and in treatment outcome. More than 10 sphingolipids and glycosphingolipids selectively mediate expressions of approximately 50 genes including c-myc, p21, c-fos, telomerase reverse transcriptase, caspase-9, Bcl-x, cyclooxygenase-2, matrix metalloproteinases, integrins, Oct-4, glucosylceramide synthase and multidrug-resistant gene 1. By diverse functions of these genes, sphingolipids enduringly affect cellular processes of mitosis, apoptosis, migration, stemness of cancer stem cells and cellular resistance to therapies. Mechanistic studies indicate that sphingolipids regulate particular gene expression by modulating phosphorylation and acetylation of proteins that serve as transcription factors (β-catenin, Sp1), repressor of transcription (histone H3), and regulators (SRp30a) in RNA splicing. Disclosing molecular mechanisms by which sphingolipids selectively regulate particular gene expression, instead of other relevant ones, requires understanding of the exact roles of individual lipid instead of a group, the signaling pathways that are implicated in and interaction with proteins or other lipids in details. These studies not only expand our knowledge of sphingolipids, but can also suggest novel targets for cancer treatments.
Keywords	RNA splicing ; acetylation ; apoptosis ; bioactive properties ; carcinogenesis ; caspase-9 ; ceramides ; gene expression ; genes ; histones ; integrins ; metalloproteinases ; metastasis ; mitosis ; multiple drug resistance ; neoplasm cells ; phosphorylation ; prostaglandin synthase ; signal transduction ; sphingosine ; stem cells ; telomerase ; transcription factors
Language	English
Dates of publication	2011-01
Size	p. 104-114.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0163-7827
DOI	10.1016/j.plipres.2010.10.003
Database	NAL-Catalogue (AGRICOLA)

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